make_graph: make_graph

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

make_graph

Description

Make correlation or cooccurrence network

Usage

make_graph(
  ret,
  num_words = 30,
  cor_threshold = 0.2,
  cooccurrence = FALSE,
  whole = FALSE,
  bn = FALSE,
  R = 20
)

Arguments

ret	biotext class object
num_words	number of words to include
cor_threshold	correlation threshold
cooccurrence	use cooccurrence
whole	return correlation or cooccurrence for whole words
bn	perform Bayesian network inference
R	parameter for boot.strength function

Details

Make correlation or cooccurrence network based on biotext object. The resulting raw network is stored in 'igraphRaw' slot in biotext object. The networks can be customized in the subsequent functions like 'process_network_gene'.

Value

biotext class object

Examples

testgenes <- c("IRF3","PNKP","DDX41","ERCC1","ERCC2","XRCC1")
obtain_refseq(testgenes) |> 
make_corpus() |> make_TDM() |> make_graph()

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.